New Associate Editors

Today we are welcoming four new Associate Editors to Methods in Ecology and Evolution. Graziella Iossa (University of Lincoln) and Theoni Photopoulou (Nelson Mandela Metropolitan University) are joining as regular Associate Editors and Simon Jarman (Unversity of Porto) and Daniele Silvestro (University of Gothenburg) will be working on Applications articles. You can find out more about all of our new Associate Editors below.

Graziella Iossa

“I am an evolutionary ecologist with broad interests in behavioural and population ecology. My research has explored reproductive strategies and the evolution of male and female reproductive traits in mammals and insects and I have used a range of techniques to study the behaviour and welfare of wildlife. I have just started to explore interdisciplinary approaches with the aim to improve our understanding of the value and role of ecosystem services in human health, specifically for antimicrobial resistance.”

Graziella’s most recent paper – Micropyle number is associated with elevated female promiscuity in Lepidoptera – investigates the evolution of the micropyle, a tiny canal which sperm use to fertilise eggs in insects. This is the first study to show that micropylar variation is driven by female promiscuity – the more micropyles her eggs have, the more choice she is likely to have over which male fathers her offspring. Also, Graziella currently holds a NERC Valuing Nature placement which aims to combine perspectives from evolutionary ecology, microbial ecology, epidemiology, ecosystem science and public health to develop a new, holistic way of understanding antimicrobial resistance

Simon Jarman

“Methods employing epigenetics, environmental DNA analysis or bioinformatics for ecological research are improving rapidly and have clear potential for future development. My research focuses on creating new methods in these areas and using them to study population biology and biodiversity. Epigenetic markers for physiological features such as biological age can be used to determine key features of population biology such as age class distribution. Environmental DNA can be used to measure species distributions; biodiversity in environmental samples; and animal diet composition. I am interested in the molecular biology and computational approaches that are required to implement these methods; as well as how they can be used to study specific ecological questions.”

In November 2016, Simon published an Open Access article in Methods in Ecology and Evolution. ‘Optimised scat collection protocols for dietary DNA metabarcoding in vertebrates‘ explains how to collect scat samples to optimise the detection of food DNA in vertebrate scat samples. More recently, Simon was the last author of ‘KrillDB: A de novo transcriptome database for the Antarctic krill (Euphausia superba)‘ – which introduces the most advanced genetic database on Euphausia superba, KrillDB, and includes comprehensive data sets of former and present transcriptome projects.

Theoni Photopoulou

“I am interested in the way biological and ecological phenomena change in space and over time. My special interest is animal movement ecology and the mechanisms behind the patterns of movement we observe. Most of the time I work on ecological questions about how animals use their environment and the resources in it, using data collected remotely with animal-attached instruments. Marine biology was my first love so I will always have a soft spot for marine systems, especially movement of large marine vertebrates, but I work on all sorts of tracking data and also some non-tracking data.”

Theoni has also recently been published in Methods in Ecology and Evolution. Her article ‘Analysis of animal accelerometer data using hidden Markov model‘ appeared in the February issue of the journal (and provided the cover image). In the paper, the authors provide the details necessary to implement and assess a hidden Markov Model in both the supervised and unsupervised learning contexts and discuss the data requirements of each case. Another of Theoni’s articles has just been accepted for publication in Frontiers in Zoology. ‘Evidence for a postreproductive phase in female false killer whales (Pseudorca crassidens)‘ investigates the evidence for postreproductive lifespan (PRLS) in the false killer whale, using a quantitative measure of PRLS and morphological evidence from reproductive tissue.

Daniele Silvestro

“I am a computational biologist and my research focuses on (macro)evolution and the development of new probabilistic models to better understand it. I am interested in the implementation of Bayesian algorithms to model evolutionary processes such as phenotypic trait evolution and species diversification and extinction. I am also interested in historical biogeography and in particular in the estimation of dispersal rates and biotic connectivity between geographic areas. A lot of my work involves developing new models and algorithms and implementing them in computer programs. I have been using both phylogenetic data and fossil occurrences to infer deep time evolutionary dynamics and I am keen to see an improved integration between paleontological and neontological data in evolutionary research.”

In his most recent article – ‘Bayesian estimation of multiple clade competition from fossil data‘ – Daniele and his co-authors explore the properties of the existing Multiple Clade Diversity Dependence implementation, which is based on Bayesian variable selection, and introduce an alternative parameterisation based on the Horseshoe prior. He was also one of the authors of ‘Mammal body size evolution in North America and Europe over 20 Myr: similar trends generated by different processes‘, published in Proceedings of the Royal Society B earlier this year.

We are thrilled to welcome Simon, Graziella, Theoni and Daniele to the Associate Editor Board and we look forward to working with them over the coming years.

Issue 8.5

Issue 8.5 is now online!

The May issue of Methods is now online!

This issue contains three Applications articles and two Open Access articles. These five papers are freely available to everyone, no subscription required.

MatlabHTK: A software interface to a popular speech recognition system making it possible for non-experts to implement hidden Markov models for bioacoustic signal processing.

 PrimerMiner: The R package PrimerMiner batch downloads DNA barcode gene sequences from BOLD and NCBI databases for specified target taxonomic groups and then applies sequence clustering into operational taxonomic units to reduce biases introduced by the different number of available sequences per species.

 BarcodingR: An integrated software package that provides a comprehensive implementation of species identification methods, including artificial intelligence, fuzzy-set, Bayesian and kmer-based methods, that are not readily available in other packages.

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Digitizing Historical Land-use Maps with HistMapR

Habitat destruction and degradation represent serious threats to biodiversity, and quantification of land-use change over time is important for understanding the consequences of these changes to organisms and ecosystem service provision.

Historical land-use maps are important for documenting how habitat cover has changed over time, but digitizing these maps is a time consuming process. HistMapR is an R package designed to speed up the digitization process, and in this video we take an example map to show you how the method works.

Digitization is fast, and agreement with manually digitized maps of around 80–90% meets common targets for image classification. We hope that the ability to quickly classify large areas of historical land use will promote the inclusion of land-use change into analyses of biodiversity, species distributions and ecosystem services.

This video is based on the Applications article ‘HistMapR: Rapid digitization of historical land-use maps in R‘ by Auffret et al. This article is freely available to anyone (no subscription required).

The package is hosted on GitHub and example scripts can be downloaded from Figshare.

Issue 8.4: Technological Advances at the Interface of Ecology and Statistics

Issue 8.4 is now online!

The April issue of Methods, which includes our latest Special Feature – “Technological Advances at the Interface of Ecology and Statistics” – is now online!

This new Special Feature is a collection of five articles (plus an Editorial from Guest Editor David Warton) inspired by the December 2015 Eco-Stats conference at the University of New South Wales in Australia. It shows how interdisciplinary collaboration help to solve problems around estimating biodiversity and how it changes over space and time.

The five articles are based on joint talks given at the conference. They focus on:

As David Warton states in his Editorial, “interdisciplinary collaboration and the opportunities offered by recent technological advances have potential to lead to interesting and sometimes surprising findings, and will continue to be fertile ground for scientists in the foreseeable future”. Meetings like Eco-Stats 15 and Special Features like this one will, hopefully, help to encourage these sorts of collaborative research projects.

All of the articles in the ‘Technological Advances at the Interface of Ecology and Statistics‘ Special Feature will be freely available for a limited time.
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Microphone Backpacks for Individual-level Acoustic Recordings

To understand the factors shaping vocal communication, we need reliable information about the communicating individuals on different levels. First, vocal behaviour should be recorded from undisturbed animals in meaningful settings. Then we have to separate and assign the individuals’ vocalisations. Finally, the precise timing of vocal events needs to be stored.

Microphone backpacks allow researchers to record the vocal behaviour of individual animals in naturalistic settings – even in acoustically challenging environments! In the video below, Lisa Gill, Nico Adreani and Pietro D’Amelio demonstrate the lightweight radio-transmitter microphone backpacks that have been developed and built at the Max Planck Institute for Ornithology, Seewiesen, Department of Behavioural Neurobiology. They show the attachment and setup of this system in detail, evaluate its behavioural effects, and discuss what makes it so useful for studying vocal communication, especially in small animals.

This video is based on the article ‘A minimum-impact, flexible tool to study vocal communication of small animals with precise individual-level resolution‘ by Gill et al.


2016 Robert May Prize Winner: Gabriella Leighton

The Robert May Prize is awarded annually for the best paper published in Methods in Ecology and Evolution by an Early Career Researcher. We’re delighted to announce that the 2016 winner is Gabriella Leighton, for her article ‘Just Google it: assessing the use of Google Images to describe geographical variation in visible traits of organisms.

‘Just Google it’ marks an important step in converting ecology to an armchair science. Many species (e.g. owls, hawks, bears) are difficult, time-consuming, expensive and even dangerous to observe. It would be a lot easier if we didn’t have to spend time, energy and risk lives having to observe organisms in the field! Continue reading

Decoupling Functional and Phylogenetic Dissimilarity between Organisms

Francesco de Bello describes the main elements of the method he has recently published in Methods in Ecology and Evolution. The method aims at decoupling and combining functional trait and phylogenetic dissimilarities between organisms. This allows for a more effective combination of non-overlapping information between phylogeny and functional traits. Decoupling trait and phylogenetic information can also uncover otherwise hidden signals underlying species coexistence and turnover, by revealing the importance of functional differentiation between phylogenetically related species.

In the video Francesco visually represents what the authors think their tool is doing with the data so you can see its potential. This method can provide an avenue for connecting macro-evolutionary and local factors affecting coexistence and for understanding how complex species differences affect multiple ecosystem functions.

This video is based on the article ‘Decoupling phylogenetic and functional diversity to reveal hidden signals in community assembly‘ by de Bello et al.


New Associate Editors

Today we are welcoming two new people to the Methods in Ecology and Evolution Associate Editor Board. Pierre Durand is joining us from the University of the Witwatersrand (South Africa) and Andrew Mahon joins from Central Michigan University (USA). You can find out more about Pierre and Andrew below.

Pierre Durand

Pierre Durand

“My research is broadly focussed on the evolution of complexity. Many of my projects are related to the evolutionary ecology of programmed cell death (PCD) in unicellular organisms; how PCD impacts microbial communities; and how the philosophy of levels of selection informs our understanding of PCD evolution. I have also examined other aspects of complexity evolution such as the origin of life and group formation in unicellular chlorophytes in response to predation. The model organisms I typically use are phytoplankton. With specific reference to submissions to Methods in Ecology and Evolution, I have used a range of methods in my research, including general cell and molecular biology tools, biochemical assays, microscopy, flow cytometry, bioinformatics and computational algorithms.”

The most current projects in Pierre’s laboratory concern: programmed cell death evolution and complexity in microbial communities; changes in phytoplankton abundance and diversity in harmful algal blooms, led by PhD candidate Andrew Ndhlovu (“A red tide forming dinoflagellate Prorocentrum triestinum: identification, phylogeny and impacts on St Helena Bay, South Africa” in review in Phycologia); and the genomics of the four-celled chlorophyte Tetrabaena socialis, led by PhD candidate Jonathan Featherson.

Andrew Mahon

Andrew Mahon

“I’m a molecular ecologist who uses genetic and genomic tools to ask questions ranging from surveillance and monitoring to biodiversity and phylogeography.  My work includes development of novel molecular detection tools and metabarcoding applications for aquatic invasive species.  I’m also interested in applying molecular tools to ask questions related to the evolution and biodiversity of benthic marine invertebrates in Antarctica.”

Andrew has recently been published in the journal Research Ideas and Outcomes (‘DNAqua-Net: Developing new genetic tools for bioassessment and monitoring of aquatic ecosystems in Europe‘) and in Environmental Science and Technology (‘Influence of Stream Bottom Substrate on Retention and Transport of Vertebrate Environmental DNA‘). He also has a manuscript in press with Ecology and Evolution (‘Geographic structure in the Southern Ocean circumpolar brittle star Ophionotus victoriae (Ophiuridae) revealed from mtDNA and single-nucleotide polymorphism data‘).

We are thrilled to welcome Pierre and Andrew to the Associate Editor Board and we look forward to working with them over the coming years.

The Field Guide to Sequence-Based Identification of Biodiversity: An Interview with Simon Creer

In a new Methods in Ecology and Evolution podcast, Georgina Brennan (Bangor University) interviews Simon Creer (Bangor University) about his article ‘The ecologist’s field guide to sequence-based identification of biodiversity‘. They talk about about where the idea for the paper came from, what it’s aim are and who will benefit from it. We hear how new sequences can improve and enhance current biomonitoring programmes (and make them quicker and cheaper).

To find out more about Sequence-based Identification of Biodiversity, read the Open Access Methods in Ecology and Evolution article ‘The ecologist’s field guide to sequence-based identification of biodiversity‘.


Issue 8.3

Issue 8.3 is now online!

The March issue of Methods is now online!

This issue contains two Applications articles and one Open Access article. These three papers are freely available to everyone, no subscription required.

 Solo: Solo audio recorders are inexpensive, easy to construct and record audible sound continuously for around 40 days. The paper also has a video tutorial explaining how to assemble the required hardware and comes with a companion website with more information.

 The third dimension: A novel design to obtain three-dimensional data on the movements of aquatic organisms at depths of up to 140m. The set-up consists of two synchronised high-speed cameras fixed to two articulated arms and can be used for any underwater applications that require synchronized video recordings of medium- to large-sized animals.

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